Locus 513

Sequence ID 3R_DroMel_CAF1
Location 1,904,886 – 1,905,055
Length 169
Max. P 0.997523
window821 window822 window823

overview

Window 1

Location 1,904,886 – 1,904,981
Length 95
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 92.89
Mean single sequence MFE -29.46
Consensus MFE -22.74
Energy contribution -22.62
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -2.80
Structure conservation index 0.77
SVM decision value 1.74
SVM RNA-class probability 0.974754
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1904886 95 + 27905053
UUAUGCCUCACAAUGGCCUGCCGCAGGUUUUUACUGCCUUCCAUUGUGUUUCUGCCUGUGUG--UGUGUUUGAUUUCUGAACCCCUUACAGGGGUAU
..(((((.((((((((......((((.......))))...))))))))......((((((.(--.(.((((.......)))).)).))))))))))) ( -28.20)
>DroSec_CAF1 63403 95 + 1
UUAUGCCUCACAAUGGCCUGCCGCAGGUUUUUACUGCCUUCCAUUGUGUUUCUGCCUGUGUG--UGUGUUUGAUUUCUGCACCCAUUACAGGGGUAU
..(((((.((((((((......((((.......))))...))))))))......((((((((--.((((..(....).)))).)).))))))))))) ( -31.60)
>DroSim_CAF1 64187 97 + 1
UUAUGCCUCACAAUGGCCUGCCGCAGGUUUUUACUGCCUUCCAUUGUGCUUCUGCCUGUGUGUGUGUGUUUGAUUUCUGCACCCAUUACAGGGGUAU
..(((((.((((((((......((((.......))))...))))))))......((((((.(((.((((..(....).)))).)))))))))))))) ( -31.90)
>DroEre_CAF1 65482 93 + 1
UUAUGCCCCACAAUGGCCUGCCGCAGGUUUUUACUGCCUUCCAUUGUAUUUCUGGCUGUG----UGUGUUUGAUUUCUACACCCAUUAGAGGGGUAU
..((((((((((((((......((((.......))))...)))))))...(((((.((.(----((((.........))))).)))))))))))))) ( -31.00)
>DroYak_CAF1 69242 91 + 1
UUAUGCCUCACAAUGGCCUGCCGCAGGUUUUUACUGCCUUCCAUUGUAUUGCUGCCUGU------GUGUUUGAUUUCUGCACCCAUUAGAGGGGUAU
.(((.(((((((((((......((((.......))))...))))))).........((.------((((..(....).)))).))...)))).))). ( -24.60)
>consensus
UUAUGCCUCACAAUGGCCUGCCGCAGGUUUUUACUGCCUUCCAUUGUGUUUCUGCCUGUGUG__UGUGUUUGAUUUCUGCACCCAUUACAGGGGUAU
..((((((((((((((......((((.......))))...)))))))..................((((..(....).))))........))))))) (-22.74 = -22.62 +  -0.12)

alignment

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secondary structure

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Window 2

Location 1,904,886 – 1,904,981
Length 95
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 92.89
Mean single sequence MFE -25.42
Consensus MFE -21.62
Energy contribution -21.78
Covariance contribution 0.16
Combinations/Pair 1.05
Mean z-score -2.44
Structure conservation index 0.85
SVM decision value 2.88
SVM RNA-class probability 0.997523
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1904886 95 - 27905053
AUACCCCUGUAAGGGGUUCAGAAAUCAAACACA--CACACAGGCAGAAACACAAUGGAAGGCAGUAAAAACCUGCGGCAGGCCAUUGUGAGGCAUAA
..(((((.....)))))................--.......((.....((((((((...((.(((......))).))...))))))))..)).... ( -26.10)
>DroSec_CAF1 63403 95 - 1
AUACCCCUGUAAUGGGUGCAGAAAUCAAACACA--CACACAGGCAGAAACACAAUGGAAGGCAGUAAAAACCUGCGGCAGGCCAUUGUGAGGCAUAA
...(((((((..((.(((...........))).--)).)))))......((((((((...((.(((......))).))...)))))))).))..... ( -24.90)
>DroSim_CAF1 64187 97 - 1
AUACCCCUGUAAUGGGUGCAGAAAUCAAACACACACACACAGGCAGAAGCACAAUGGAAGGCAGUAAAAACCUGCGGCAGGCCAUUGUGAGGCAUAA
.....(((((..((.(((...........))).))...)))))..(...((((((((...((.(((......))).))...))))))))...).... ( -24.90)
>DroEre_CAF1 65482 93 - 1
AUACCCCUCUAAUGGGUGUAGAAAUCAAACACA----CACAGCCAGAAAUACAAUGGAAGGCAGUAAAAACCUGCGGCAGGCCAUUGUGGGGCAUAA
.((((((......))).))).............----....(((.....((((((((...((.(((......))).))...)))))))).))).... ( -27.40)
>DroYak_CAF1 69242 91 - 1
AUACCCCUCUAAUGGGUGCAGAAAUCAAACAC------ACAGGCAGCAAUACAAUGGAAGGCAGUAAAAACCUGCGGCAGGCCAUUGUGAGGCAUAA
.(((((.......)))))..............------.......((..((((((((...((.(((......))).))...))))))))..)).... ( -23.80)
>consensus
AUACCCCUGUAAUGGGUGCAGAAAUCAAACACA__CACACAGGCAGAAACACAAUGGAAGGCAGUAAAAACCUGCGGCAGGCCAUUGUGAGGCAUAA
.(((((.......)))))........................((.....((((((((...((.(((......))).))...))))))))..)).... (-21.62 = -21.78 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,904,948 – 1,905,055
Length 107
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 78.67
Mean single sequence MFE -25.62
Consensus MFE -15.89
Energy contribution -16.61
Covariance contribution 0.72
Combinations/Pair 1.25
Mean z-score -1.99
Structure conservation index 0.62
SVM decision value 0.86
SVM RNA-class probability 0.869302
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1904948 107 + 27905053
UGUGUUUGAUUUCUGAACCCCUUACAGGGGUAUGCUGAGUUUUGG--CAUACAC----AUAAACUUGAAAAGAUAUAGAACACAAAUAUGAACUUAUAAGCUCGAAAAGGUAA
(((((((....(((....(((.....)))((((((..(...)..)--)))))..----............)))....)))))))....(((.((....)).)))......... ( -23.10)
>DroSec_CAF1 63465 107 + 1
UGUGUUUGAUUUCUGCACCCAUUACAGGGGUAUGCUGAGUUGUGG--CAUACAU----AUAAACUCGAAAAGAUAUAGAACUCAAACAUGAACCUAUAAGCUCGAAAGGGUAA
.((((((((.(((((..(((......)))(((((((.......))--)))))..----.................))))).))))))))..........((((....)))).. ( -32.20)
>DroSim_CAF1 64251 107 + 1
UGUGUUUGAUUUCUGCACCCAUUACAGGGGUAUGCUGAGUUUUGG--CAUACAU----AUAAACUCGAAAAGAUAUAGAACUCAAACAUGAACCUAUAAGCUCGAAAGGGUAA
.((((((((.(((((..(((......)))((((((..(...)..)--)))))..----.................))))).))))))))..........((((....)))).. ( -32.60)
>DroEre_CAF1 65542 87 + 1
UGUGUUUGAUUUCUACACCCAUUAGAGGGGUAUGCUGAGUUUGGGA-CAUGUAC----ACAUACUUGAAAAGAAAUAGAGCUCAA---------------------AGGGUAG
((.((((.((((((..((((.......)))).....((((.(((..-......)----.)).))))....)))))).)))).)).---------------------....... ( -16.40)
>DroYak_CAF1 69301 112 + 1
-GUGUUUGAUUUCUGCACCCAUUAGAGGGGUAUGCCGAGUUCUGAAGUAUAUACAUAUAUAUAUUUGAAAAGAUAUAGAGCUCAAACAUUAACUUAUAUGAUCAAAAGGGUAG
-............(((.(((......))))))((((((((((((..(((((....))))).(((((....)))))))))))))...(((........)))........)))). ( -23.80)
>consensus
UGUGUUUGAUUUCUGCACCCAUUACAGGGGUAUGCUGAGUUUUGG__CAUACAC____AUAAACUUGAAAAGAUAUAGAACUCAAACAUGAACCUAUAAGCUCGAAAGGGUAA
.((((((((.(((((.((((.......))))....(((((((..................)))))))........))))).))))))))........................ (-15.89 = -16.61 +   0.72)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:59 2006